vapB17 Family assigned · medium auto-curated
H37Rv Rv2526 · MTBC0 mtbc0_002690 ·
75 aa · 2873981–2874208 (+) ·
RefSeq NP_217042.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | antitoxin VapB17 |
|---|---|
| MTBC0 PGAP re-annotation | type II toxin-antitoxin system VapB family antitoxin |
| Revised (this work) | Type II toxin-antitoxin system VapB family antitoxin. Pfam: VapB_antitoxin (PF09957.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ49
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative antitoxin VapB17 |
| Curated function | Putative antitoxin component of a possible type II toxin-antitoxin (TA) system. The cognate toxin is VapC17. |
UniProt still lists this protein as Putative antitoxin VapB17; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Bacterial antitoxin of type II TA system, VapB |
| Orthologous group | 2EV0F |
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains) pseudogene candidate
| pN/pS | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 26.12% of strains (37931) · clonal |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
VapB_antitoxin | PF09957.16 | 2.5e-07 | 4–44 | Bacterial antitoxin of type II TA system, VapB |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC17 (ribonuclease VapC17), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2527 vapC17 |
ribonuclease VapC17 | 887 | 887 ctx | neighborhood:882 |
Rv0656c vapC6 |
ribonuclease VapC6 | 655 | 51 | textmining:652 |
Rv0549c vapC3 |
ribonuclease VapC3 | 515 | 51 | textmining:510 |
Rv1655 argD |
acetylornithine aminotransferase | 513 | 47 | textmining:510 |
Rv1657 argR |
arginine repressor | 443 | 47 | textmining:440 |
Rv1653 argJ |
bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase | 441 | 47 | textmining:438 |
Rv2819c csm5 |
CRISPR type III-associated RAMP protein Csm5 | 440 | 47 | textmining:437 |
Rv1659 argH |
argininosuccinate lyase | 438 | 47 | textmining:435 |
Rv0624 vapC30 |
ribonuclease VapC30 | 439 | 46 | textmining:437 |
Rv2653c |
toxin | 437 | 45 | textmining:435 |
Rv2494 vapC38 |
ribonuclease VapC38 | 432 | 45 | textmining:430 |
Rv0748 vapB31 |
antitoxin VapB31 | 657 | 44 | textmining:656 |
Rv1720c vapC12 |
ribonuclease VapC12 | 628 | 44 | textmining:627 |
Rv1397c vapC10 |
ribonuclease VapC10 | 625 | 44 | textmining:624 |
Rv3408 vapC47 |
ribonuclease VapC47 | 545 | 44 | textmining:544 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: antitoxin VapB17
- MTBC0 PGAP product: type II toxin-antitoxin system VapB family antitoxin
- Pfam (hmmscan --cut_ga): VapB_antitoxin PF09957.16 (E=2e-07)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217042.1)
- Domains: Pfam-A via hmmscan --cut_ga — VapB_antitoxin (PF09957.16)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
2EV0F - Curated reference: UniProt P9WJ49 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
19 functional partner(s); context anchor
vapC17 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002690|Rv2526|vapB17 MTVKRTTIELDEDLVRAAQAVTGETLRATVERALQQLVAAAAEQAAARRRRIVDHLAHAGTHVDADVLLSEQAWR